Hi - no, it was correct in the original email.
Cheers.
On 9 Mar 2007, at 06:02, Ping-Hong Yeh wrote:
> in #10117 mail (see below) for coregistering target to MNI_152
> using flirt,
> should "-init flirtaffinetransf.mat" for replacing line 69 be a
> typo of
> "-omat flirtaffinetransf.mat" ?
>
> i.e.
> $FSLDIR/bin/flirt -in target.hdr -ref $M -out
> target_to_MNI152.hdr -omat flirtaffinetransf.mat
> -applyxfm
>
> but not
>
> $FSLDIR/bin/flirt -in target.hdr -ref $M -out
> target_to_MNI152.hdr -init flirtaffinetransf.mat
> -applyxfm
>
> Thanks.
>
>
> #10117
> unfortunately, there is no easy way (so far) to
> convert an areg .dof into a flirt .mat... So the best
> way to continue the tbss preprocessings is to register
> your diffusion images in two steps.
>
> You can do so by editing tbss_3_postreg script and by:
>
> 1) replacing the areg transformation from the best
> target to the MNI152 by the flirt one in the
> tbss_3_postreg script:
>
> - erase line 68
> - replace line 69: ${D}/transformation target.hdr
> target_to_MNI152.hdr -dofin target_to_MNI152.dof
> -linear -target $M
>
> by -> $FSLDIR/bin/flirt -in target.hdr -ref $M -out
> target_to_MNI152.hdr -init flirtaffinetransf.mat
> -applyxfm
>
> 2) separating the two transformations applied to your
> diffusion images:
>
> - replace line 76: ${D}/transformation2 ${f}.hdr
> ${f}_to_${best}_nonlinear_hr.hdr -dofin2
> ${f}_to_${best}_nonlinear.dof -dofin1
> ../stats/target_to_MNI152.dof -linear -target
> ../stats/$M
>
> by -> ${D}/transformation ${f}.hdr
> ${f}_to_${best}_tmp.hdr -dofin
> ${f}_to_${best}_nonlinear.dof -linear -target
> ${best}.hdr
> followed by -> $FSLDIR/bin/flirt -in
> ${f}_to_${best}_tmp.hdr -ref $M -out
> ${f}_to_${best}_nonlinear_hr.hdr -init
> flirtaffinetransf.mat -applyxfm
------------------------------------------------------------------------
---
Stephen M. Smith, Professor of Biomedical Engineering
Associate Director, Oxford University FMRIB Centre
FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK
+44 (0) 1865 222726 (fax 222717)
[log in to unmask] http://www.fmrib.ox.ac.uk/~steve
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